rs2915954

Variant names:

• chr19-38506000-A-G
• rs2915954
• NM_000540.3:c.8541+54A>G

Your query was ambiguous. Multiple possible variants found:

• chr19-38506000-A-G
• chr19-38506000-A-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000540.3(RYR1):​c.8541+54A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 1,479,342 control chromosomes in the GnomAD database, including 60,377 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.32 (8434 hom., cov: 29)
  • Exomes 𝑓: 0.25 (51943 hom.)
• Consequence: RYR1 NM_000540.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2 O:1
• Conservation: PhyloP100: -2.60

Genes affected

RYR1 (HGNC:10483): (ryanodine receptor 1) This gene encodes a ryanodine receptor found in skeletal muscle. The encoded protein functions as a calcium release channel in the sarcoplasmic reticulum but also serves to connect the sarcoplasmic reticulum and transverse tubule. Mutations in this gene are associated with malignant hyperthermia susceptibility, central core disease, and minicore myopathy with external ophthalmoplegia. Alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 19-38506000-A-G is Benign according to our data. Variant chr19-38506000-A-G is described in ClinVar as [Benign]. Clinvar id is 133229.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-38506000-A-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RYR1	NM_000540.3	c.8541+54A>G		intron_variant	Intron 54 of 105	ENST00000359596.8	NP_000531.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RYR1	ENST00000359596.8	c.8541+54A>G		intron_variant	Intron 54 of 105	5	NM_000540.3	ENSP00000352608.2
RYR1	ENST00000355481.8	c.8541+54A>G		intron_variant	Intron 54 of 104	1		ENSP00000347667.3
RYR1	ENST00000594335.5	n.1992+54A>G		intron_variant	Intron 15 of 48	1		ENSP00000470927.2
RYR1	ENST00000599547.6	n.8541+54A>G		intron_variant	Intron 54 of 79	2		ENSP00000471601.2

Frequencies

GnomAD3 genomes AF: 0.324 AC: 48749 AN: 150678 Hom.: 8397 Cov.: 29

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.334

GnomAD4 exome AF: 0.249 AC: 331117 AN: 1328542 Hom.: 51943 AF XY: 0.256 AC XY: 170086 AN XY: 664558

Gnomad4 AFR exome AF: 0.414

Gnomad4 AMR exome AF: 0.385

Gnomad4 ASJ exome AF: 0.242

Gnomad4 EAS exome AF: 0.332

Gnomad4 SAS exome AF: 0.438

Gnomad4 FIN exome AF: 0.285

Gnomad4 NFE exome AF: 0.217

Gnomad4 OTH exome AF: 0.273

GnomAD4 genome AF: 0.324 AC: 48848 AN: 150800 Hom.: 8434 Cov.: 29 AF XY: 0.331 AC XY: 24360 AN XY: 73604

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.339

Alfa AF: 0.281 Hom.: 693

Bravo AF: 0.332

Asia WGS AF: 0.483 AC: 1671 AN: 3470

ClinVar

Significance: Benign

Submissions summary: Benign:2 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2 Other:1

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

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RYR1 database

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.17
DANN	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2915954; hg19: chr19-38996640;